5J5X

Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1416


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions.

Ivan, T.Enkvist, E.Viira, B.Manoharan, G.B.Raidaru, G.Pflug, A.Alam, K.A.Zaccolo, M.Engh, R.A.Uri, A.

(2016) Bioconjug.Chem. 27: 1900-1910

  • DOI: 10.1021/acs.bioconjchem.6b00293
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) ...

    The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) PPIs tends to fall short due to the flat and wide interfaces of PPIs. Here we propose a biligand approach for disruption of strong PPIs. The potential of this approach was realized for disruption of the tight-binding (KD = 100 pM) tetrameric holoenzyme of cAMP-dependent protein kinase (PKA). Supported by X-ray analysis of cocrystals, bifunctional inhibitors (ARC-inhibitors) were constructed that simultaneously associated with both the ATP-pocket and the PPI interface area of the catalytic subunit of PKA (PKAc). Bifunctional inhibitor ARC-1411, possessing a KD value of 3 pM toward PKAc, induced the dissociation of the PKA holoenzyme with a low-nanomolar IC50, whereas the ATP-competitive inhibitor H89 bound to the PKA holoenzyme without disruption of the protein tetramer.


    Organizational Affiliation

    Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia.,The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway.,Department of Physiology, Anatomy and Genetics, University of Oxford , OX1 3QX Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
351Homo sapiensMutation(s): 0 
Gene Names: PRKACA (PKACA)
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Go to Gene View: PRKACA
Go to UniProtKB:  P17612
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
47P-AZ1-DAL-DAR-DAR-DAR-DAR
B
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6J9
Query on 6J9

Download SDF File 
Download CCD File 
A
4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine
C10 H13 N5
LZSXQBNNRGZPES-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
6J9
Query on 6J9
B
NON-POLYMERC10 H13 N5

--

NH2
Query on NH2
B
NON-POLYMERH2 N

--

SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
ZEU
Query on ZEU
B
NON-POLYMERC9 H18 O3

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.237 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.023α = 90.00
b = 127.023β = 90.00
c = 89.631γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-31
    Type: Database references
  • Version 2.0: 2019-06-19
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary